/feed _forum.php?forum_id=4441 Full instructions for installing and using the RSS app with Slack feed to Slack can be found in the Slack Help Center. Close function confirmDel() var agree=confirm("Proceed with deletion? ");if (agree) return true ;else return false ;function manageattachments(url,del) var newwindow;if (del=="yes") if (!confirmDel())return;newwindow = window.open(url, 'Attach', 'statusbar=no,menubar=no,toolbar=no,scrollbars=yes,resizable=yes,width=600,height=480');if (window.focus) newwindow.focus()Showing 1-75 of 177 postsStart New Topic Display: Threaded PostsFlat PostsThreaded TitlesActive TopicsjQuery(".hide-with-javascript").css("display","none");Results per page: Show 25Show 50Show 75Show 100jQuery(".hide-with-javascript").css("display","none");1 2 3 Next >Oct 7, 2014 08:10 PM Chris RordenWelcome to Open-DiscussionWelcome to Open-DiscussionQuote & Reply Reply Oct 30, 2014 03:10 PM Bastian ChengWhite Matter AtlasHi!First of all: what a great tool! I've been looking for an intuitivevisualization program for a long time.One questions: Are the overlays from a standard white mattertractography atlas available?I found them in the connectivity explorer by denis ducreux and waswondering if one could use them in this software.My aim would be to compare own tracking results to locations ofwhite matter tracts.best regards,BastianQuote & Reply Reply Nov 22, 2014 12:11 PM Chris RordenRE: White Matter AtlasThanks for your comments. I think you have a couple of options forwhite matter tractsConnectopedia is a fantastic tool from Denis Ducreux that uses theMRIcroGL engine for rendering. You can use it on its own or use theimages with other tools. You can use the images withinConnectopedia or with other tools (as I recall, with OSX you haveto 'show package contents' to see the images). These are highquality maps from a single individual: Marco Catani and his team have created some nice probabilisticwhite matter maps based on a group of indiviuals. & Reply Reply Nov 22, 2014 03:11 PM Bastian Cheng RE: White Matter AtlasHi Chris! Those are excellent suggestions! Thank you again for yourhelp!BastianQuote & Reply Reply Dec 28, 2014 11:12 PM Xiaowei SongDoes MRIcroGL have a cmd interface?Hi, Chris,thanks for the great 3D displaying tool.Does or will MRIcroGL have a cmd interface like caret andcaret_command?Best,XiaoweiQuote & Reply Reply Sep 5, 2015 01:09 PM Chris RordenRE: Does MRIcroGL have a cmd interface?Hello- MRIcroGL has a full scripting language, you can see examples here You can have MRIcroGL run these scripts when it launches, and thisallows other programs to control MRIcroGL (for example havingMatlab batch a large set of images). In particular, with Matlab youwould use the "system" function to launch MRIcroGL. There are twomethods:1.) If you place a text file named 'startup.gls' in MRIcroGL'sscript folder it will run this script when the program launches.2.) You can pass the name of a script file to MRIcroGL at launch,for example "MRIcroGL /myDir/myScript.gls". This will causeMRIcroGL to run the specified script. a.) A very useful function for these scripts is the "quit;"command. Put this in the last line of your script and MRIcroGL willshut down once it has completed running your script. This is usefulif you want to save a batch of bitmaps and do not want any userinteraction. However, be aware that if a user opens and runs ascript from the graphical user interface with a "quit" the programwill shut down as soon as it is done. In particular, if you make a"startup.gls" script with "quit" in it and do not delete this fileafter it is executed users will not be able to run MRIcroGLgraphically: whenever it is launched it will auotmatically run thestartup script and then quit.3.) Be aware that with OSX the script and application files areboth hidden in the application package, and in general OSX is morefinicky about running items (the interface may give you a warning).In any case, with OSX you would call the script like this"/osx/MRIcroGL.app/contents/MacOS/MRIcroGL/osx/MRIcroGL.app/script/basic.gls "Quote & Reply Reply Sep 5, 2015 01:09 PM Chris RordenBeta test for new releaseI am about to release a new version of MRIcroGL. If anyone wishesto test this, you can download it from and find out about the new features here unless bugs are reported, this will be the new stable release.-cQuote & Reply Reply Dec 18, 2015 07:12 PM Sirous Nekooei - MUMSRE: Beta test for new releaseDear ChrisFirst of all, I'd like to thank you so much for this usefulsoftware.I want to use it for presentation of fMRI overlays.As you know, physicians are used to view images in radiologicorientation. So I'd like to print them like that.In the previous versions, there was an R/L flip option (in MRIcroand MRIcron) but in MRIcroGL, which has a better interface topresent mosaic visualization, the R/L option is missing.Is there a specific reason for that?SirousQuote & Reply Reply Mar 8, 2016 04:03 PM gaeljDeeper activationsHi,I've been unsuccessfully looking for the 'search depth' setting ofmricron in mricroGL. I love the quality of the render in mricroGL,but have not yet found a satisfactory way of displaying activationsthat are slightly under the brain surface.I join an illustration of what I can do with mricron and the best Ican achieve with mricroGL. Note that the parietal activations arenot easy to see on the mricroGL rendering, do you have a way ofimproving this that I did not see ?Thank you for your help.Gaël.Attachment: render.png Quote & Reply Reply Apr 5, 2016 09:04 PM Andre Peres - Brain Institute - Federal University of Rio Grande do Norte - UFRNMRIcroGL issuesHello,I'm using the last version of MRIcroGL on iMac OS X 10.9.5, and onLubuntu 14.4. However, I found some problems running on bothsystems: On Mac, when I try to run a script, the mac crashes, and Ineed to reboot pressing the power button. On linux, it's happeningsomething weird, when I type something in the interface (max/minIntensity) or in the script window the letters are typedtwice,i.e., if I press just one time the letter A, it's typed AA,the same occur with the numbers.I have tried all the three versions available on the website, butdoesn't work.Please, could you help me?Quote & Reply Reply May 10, 2016 09:05 PM rachelnakoShowing ovarlay withsignificant t-values onlyDear all,I am just a student and quite new to this software (I'm noteven sure if this is the right place to ask). I also use SPM and Iwas wondering if it is possible to show the significantly differentvoxels, after bonferroni correction in MRIcroGL like I can in SPM ? And is it possible to show this in the ROIs as well? Putdifferently: how can I reduce the presence of type I errors inimages in MRIcroGL? Is that what the Min / Max values are for?I would like to show these clusters in 3D, as MRIcroGL offers.Many thanks in advance & Kind Regards,RachelQuote & Reply Reply Jun 19, 2016 05:06 PM Sebastian UrchsTrojan flagged on most recent windows zipHi,I just downloaded the windows zipfrom got a warning from my antivir (360 security) that the filecontained a trojan:Type:Threat detected in compressed filesDescription:C:\Users\Sebastian\Downloads\windows.zip=>mricrogl\dcm2niix.exe: Win32/Trojan.97aScan Engine:360 Cloud Scan EngineLocation:C:\Users\Sebastian\Downloads\windows.zipSuggestion:Quarantined filesPretty sure it's a false flag but in any case I'd like to let youknow.Best,SebastianQuote & Reply Reply Jun 30, 2016 08:06 PM Carl Helmick - Dalhousie University, Psychiatry Deptdcm2niix-5May2016 ignores -o flagThe command-line program dcm2niix does not respect the "-o flag. Would it be possible to compile and release a new version ofdcm2niix?Thanks!CarlQuote & Reply Reply Aug 30, 2016 04:08 PM Niels FockeRE: dcm2niix-5May2016 ignores -o flagI can confirm this behaviour - the -o flag seems to be ignored bythe May05 version (Linux, 64bit). A fix would be appreaciated,since I would like to use this software in a batched/automated way.Thanks. NielsQuote & Reply Reply Oct 3, 2016 01:10 PM Benjamin Wagner - UT Southwestern Medical CenterRE: dcm2niix-5May2016 ignores -o flagI hope a fixed release of this will come out soon. I need the5 May version for handle some Philips data but also need the -o forbatch processing. If not a release of the whole MRIcroGLmaybe just the affected dcm2niix binaries?BenQuote & Reply Reply Oct 12, 2016 02:10 PM Benjamin Wagner - UT Southwestern Medical Center30-Sept-2016 dcm2niix requires GLIBC_2.14The dcm2niix included with the referenced release will not run onRHEL 6.6. It fails with the error:dcm2niix: /lib64/libc.so.6: version 'GLIBC_2.14' not found(required by dcm2niix)MRIcroGL does work. I looks as if the two executables werecompiled on different machines:[]$ file 'which dcm2niix'/project/software/mricron/20160930gl/dcm2niix: ELF 64-bit LSBexecutable, x86-64, version 1 (SYSV), dynamically linked (usesshared libs), for GNU/Linux 2.6.32, stripped[]$ file 'which MRIcroGL'/project/software/mricron/20160930gl/MRIcroGL: ELF 64-bit LSBexecutable, x86-64, version 1 (SYSV), dynamically linked (usesshared libs), for GNU/Linux 2.4.0, strippedAny chance of dcm2niix being compiled for a lower GLIBC?BenQuote & Reply Reply Oct 14, 2016 04:10 PM Mo BenMIRcroGL Absolute Intensity Calculation?Hello All,I'm working on a virtual reality NIfTI viewer and I'm usingsome of the color scheme look up tables from this project asreference.The LUT files in the source use an absolute value for min and maxintensity, matching the values displayed in the top left corner ofthe MIRcroGL viewer. For example, CT_Lungs uses the followingvalues: [FLT] min=-902 max=-305I'm not sure how these values are calculated, or how the NIfTIfiles are mapped to this scale. I did some analyzing of the headerfile and data. It seems they are encoded from [0,255] and theheader files' glmin and glmax values match those values. Meanwhilecl_min and cl_max are unused.How are these absolute values calculated? Am I missing somethingobvious here?Quote & Reply Reply Oct 14, 2016 04:10 PM Mo BenRE: MIRcroGL Absolute Intensity Calculation?Did some more digging and figured it out. Using the scl_slopand scl_inter values you can find the scaled values.Quote & Reply Reply Oct 16, 2016 07:10 AM Mo BenRE: MIRcroGL Absolute Intensity Calculation?Ok, opening this back up.Some of the .clut (Color scheme source look up tables) files havemin and max set to 0. I expected those color schemes to use thelowest and highest intensity for each file they were used on, butit turns out it is determining a seemingly arbitrary range ofintensity, which is different for each file.Does anyone know how the minimum and maximum intensity for thosecolor schemes is calculated? For example the default grayscale whenused on the ch256.nii file uses a minimum of 40 and maximum of120, even though the intensity can go down to 0.Quote & Reply Reply Oct 27, 2016 03:10 PM Javier Juan-Albarracín - Universitat Politècnica de València (UPV)dcm2niix ignores compresion flagdcm2niix seems to ignore the -z compression flag (at least inwindows). I have also checked that pigz.exe is in the same folderthan dcm2niix.exe but the output is always a .nii file. I haveproved with "-z y" and without explicitly setting the flag but theoutput is always an uncompressed NIfTI. Any idea?Thanks! JavierQuote & Reply Reply Oct 31, 2016 04:10 PM Cecil YenRE: 30-Sept-2016 dcm2niix requires GLIBC_2.14I also found the same issue here. Our institute was still using RedHat/CentOS 6 as our working hose. So, we can't upgrade to RedHat/CentOS 7 soon. Is there any reason that dcm2niix has to bebuilt against newer GLIBC?CecilQuote & Reply Reply Nov 1, 2016 03:11 PM Chris RordenRE: 30-Sept-2016 dcm2niix requires GLIBC_2.14You can download a version of dcm2niix compiled on Centos 6.6(kernel 2.6.18; GCC 4.4.7) dcm2niix and MRIcroGL were compiled on the same machine, butgenerated with different compilers (dcm2niix = gcc, MRIcroGL =fpc). GLIBC 2.14 was released in 2011 and Linux 2.6.32 in 2009, somy compiled software should work on most modern Linux systems. Icompiled the project on NeuroDebian 8.0 (kernel 2.6.32; GCC 4.9.2).I think there will always be a tradeoff in distributing compiledLinux software between maximum compatibility versus benefits of newversions. If you want a version optimized for your system you can alwayscompile your own by getting the code from GitHub ( ), and running the "make" command in the "console" folder.Quote & Reply Reply Nov 1, 2016 03:11 PM Chris RordenRE: Deeper activationsWith the latest version of MRIcroGL (30Sept2016) you controloverlay depth with the "overDistance" and "overAlpha" sliders(assuming you are using the "Default" shader). You may also want toswitch the shader from "Default" to one of the "overlay_*" shaders(e.g. overlay_shell or overlay_glass).For visualizing deep activations, a surface renderer (e.g. SurfIce) displaying a mesh may be nicer than a volume renderer(MRIcroGL): :MainPage#Overlay_a_normalized_SPM_or_FSL_statistical_map_that_has_been_converted_to_an_iso-surface_mesh :MainPage#Scripting_a_mesh_overlayQuote & Reply Reply Nov 1, 2016 03:11 PM Chris RordenRE: MRIcroGL issuesCan I suggest you download the latest versions (30Sept2016) andtell me if your issues persist?Quote & Reply Reply Nov 1, 2016 03:11 PM Chris RordenRE: Showing ovarlay withsignificant t-values onlySure, just adjust the minimum and maximum values in the "Overlay"panel (see the "Overlays" section of the manual).Attachment: threshold.jpg Quote & Reply Reply Nov 1, 2016 04:11 PM Chris RordenRE: Trojan flagged on most recent windows zipAppears to be a false positive - my machine hasSymantec ProtectionSuite and I compile straight from cygwin. Furthermore, a scan ofthat file with the 56 virus detection tools usedby does not find any problems. Iassume your 360 security will have an update to resolve this.Quote & Reply Reply Nov 3, 2016 03:11 PM Chris RordenRE: dcm2niix ignores compresion flagMake sure the executable pigz.exe is in the same folder as thedcm2niix.exe. Both executables are included with MRIcroGL. dcm2niixgenerates a warning if you request gzipped output but it can notfind pigz. By the way, future versions of the Windows software willuse the internal compressor if it can not find pigz, similar to thecurrent Linux/OSX releases. In general, the multithreaded pigz ismuch faster than the single-threaded internal compressor, but ifyou are storing data to a slow (networked) disk, you may find theinternal compressor faster (since using pigz requires the softwareto first save the uncompressed data to disk and then compress thatfile, while the internal compressor saves the data compressed in asingle pass). This explains why Linux/OSX versions of dcm2niixallow you to specify three options for gzip: "-z y", "-z i", "-zn", that will (respectively) gzip output (using pigz if found),gzip output (using internal compressor) or not gzip the output.--------- Example 1 : pigz found ---------c:\mricrogl>dcm2niix -z Y c:\tst_t1Chris Rorden's dcm2niiX version 10oct2016 (32-bit Windows)Found 192 DICOM image(s)Convert 192 DICOM asc:\tst_t1\20140228152127_T1_mprage_ns_sag_p2_iso_1.0mm__4 (256x256x192x1)compress: ".\pigz" -n -f"c:\tst_t1\20140228152127_T1_mprage_ns_sag_p2_iso_1.0mm__4.nii"Conversion required 1.781000 seconds.--------- Example 2 : pigz not found ---------c:\mricrogl>dcm2niix -z Y c:\tst_t1Compression requires pigz.exe in the same folder as the executableChris Rorden's dcm2niiX version 10oct2016 (32-bit Windows)Found 192 DICOM image(s)Convert 192 DICOM asc:\tst_t1\20140228152127_T1_mprage_ns_sag_p2_iso_1.0mm__4 (256x256x192x1)Conversion required 0.234000 seconds.Quote & Reply Reply Nov 27, 2016 12:11 PM Christian KaufmannDicom to Nifti / dcm2niix / Slice timingDear all,is it possible to include DICOM slice time information (fromSiemens MR) in Nifti file header? It might be possible withdcm2niix but I might have missed the right flag. Any advice ishighly appreciated, thank you.ChristianQuote & Reply Reply May 27, 2017 11:05 AM Chris RordenRE: Dicom to Nifti / dcm2niix / Slice timingHello- dcm2niix with put the Siemens slice order information intothe NIfTI slice_order tag. An exception to this is if your data wasacquired with multiband, where the slice order can not becompletely described by the 6 slice order options In this case, you can look at the "SliceTiming" field of the BIDSjson header to determine the order.Quote & Reply Reply May 27, 2017 06:05 PM SUDHAKAR MISHRA - Indian Institute of Information Technology AllahabadMRIcroGL with RIs it possible to use MRIcroGL with R.Quote & Reply Reply May 28, 2017 05:05 AM SUDHAKAR MISHRA - Indian Institute of Information Technology AllahabadOverlayload in MRIcroGLWhat is this overlayload in MRIcroGL. In the example scripts'Motor' is given. If I put some other brain region it throws error.If anyone has any clue about how to put this entry, please postit. Any help would be great.Quote & Reply Reply Jun 1, 2017 12:06 AM Chris RordenRE: MRIcroGL with RMRIcroGL is a standalone executable, so you can not wrap it R.However, it does have a scripting language that you can use tolaunch it, open images, save bitmaps and even quit. This allows youto control it with any programming language that allows you toexecute an external program - I provide samples for shell scripts,Matlab and Python. A web search for "R execute external program"will show you how to do this. :MainPage#Scripting_from_the_command_line_and_other_programsQuote & Reply Reply Jun 1, 2017 12:06 AM Chris RordenRE: Overlayload in MRIcroGLYou can find out what MRIcroGL scripting functions do by readingthe included PDF manual, or by selecting the command in thescripting window. When you insert a command using the scriptingwindow you will see usage notes appear at the bottom of the window.For example, if you choose the Insert/Overlay/Overlayload menu itemyou will see:OVERLAYLOAD (lFilename: string): integer; Will add the overlaynamed filename and return the number of the overlay.The software comes with a sample NIfTI image named "motor.nii.gz"which shows motor activation as observed in an fMRI task. If youwant to load a different image you will need to provide its name,for example OverlayLoad('c:\mydir\myimg.nii'). You could shortenthis to OverlayLoad('myimg') if the image is in the same folder asthe MRIcroGL executable.Quote & Reply Reply Jun 15, 2017 03:06 PM Lars Kasper - Translational Neuromodeling Unit, IBT, University of Zurich and ETH ZurichBitmap-saving and image smoothing optionsDear Chris,I am a big fan of the whole MRIcro*-series - which for my purposesprovide the best available viewers. Thank you for making thisavailable to us. Recently, I became very interested in thescripting functionality of MRIcroGL.I encountered two issues/questions lately:1) When I choose one axial slice for plotting, use File -> Saveor SAVEBMP('filename'), while the Preferences -> BitmapZoom is greater than one, I get horizontal black bars in theexported png. E.g., 1 in the center for zoom 2, but 5 parallel onesfor zoom 10. My workaround is to set the bitmap zoom level to 1 inmricrogl.ini (or can I change it via scripting?).2) Compared to other viewers, my 2D axial slices look somehowsmoothed (the underlay, not the overlays), i.e. I cannotdistinguish the pixels any more. Is there an implicit smoothingperformed in 2D as well that I can adjust and switch off via ascript?Thank you very much for your help and once more for this greatcontribution to the community!Below you find my system specs and the script, attached the bitmapsI am referring to.Kind regards,Lars Here are my system specs:Mac OS Sierra 10.12.5MRIcroGL, May 5, 2016MacBook Air 2013 with one external monitor connected (1680x1050)And here the generating script:beginRESETDEFAULTS; SHADERQUALITY1TO10(10);LOADIMAGE('meanaspOutFmri1.nii');CONTRASTMINMAX(0.1,1.1);OVERLAYLOADSMOOTH(false);OVERLAYTRANSPARENCYONOVERLAY(0);OVERLAYTRANSPARENCYONBACKGROUND(0);OVERLAYCOLORFROMZERO(false);SHADERNAME('minimal');COLORBARVISIBLE(false);OVERLAYLOAD('spmT_0001.nii');OVERLAYMINMAX(1,3.7, 5);OVERLAYLOAD('spmT_0001.nii');OVERLAYMINMAX(2, -5, -3.7);OVERLAYLOAD('../edge0.10_MultiechoUmpire1mm.nii');OVERLAYMINMAX(3,0, 2);OVERLAYLOAD('edge0.10_MultiechoUmpire1mm.nii');OVERLAYMINMAX(4, 0,2);OVERLAYLOAD('../edge0.10_MultiechoUmpire1mm.nii');OVERLAYMINMAX(5,0, 1.5);OVERLAYLOAD('../edge0.10_MultiechoUmpire1mm.nii');OVERLAYMINMAX(6,0, 2);OVERLAYVISIBLE(1, true); OVERLAYVISIBLE(2, true);OVERLAYVISIBLE(3,false);OVERLAYVISIBLE(4, false);OVERLAYVISIBLE(5, true);OVERLAYVISIBLE(6,false);OVERLAYMASKEDBYBACKGROUND(false);MOSAIC('L- H -0.1 V 0 A0.39');SAVEBMP('spOutFmri1_overlay1_preproc1_slicepack3_withEdge.png');end.Attachment: test2.png Quote & Reply Reply Jun 18, 2017 08:06 AM Lars Kasper - Translational Neuromodeling Unit, IBT, University of Zurich and ETH ZurichRE: Bitmap-saving and image smoothing optionsDear Chris,I just tried the new version you sent me. It works perfectly, thankyou so much. Will this be in an upcoming release of MRICroGL?- Images are in native resolution- BMPZOOM scales them correctly, no black bars any more!- SHARPEN works in a script- The exported pngs look much crisper, even without sharpen!- Retina-Display option does not alter the images (I guess becauseI don't have a retina screen :-))All the best, and thank you again, this boosts my workflow,LarsQuote & Reply Reply Jun 22, 2017 05:06 PM Chris RordenRE: Bitmap-saving and image smoothing optionsThese features are all included in the 21 June 2017 release nowavailable on NITRC. The specific changes for your situation: 1.) When you save or copy MOSAIC images, the image resolutionis based on the voxel size of your images, not the resolution ofyour screen. Therefore, BMPZOOM=1 has precisely the dimensions ofyour background image whil BMPZOOM=2 double it. This reducesblurring common with non-integer scaling. 2.) BMPZOOM and SHARPEN functions added to the scriptinglanguage. In the past you could only choose BMPZOOM through the GUIPreferences panel and SHARPEN with the View/Sharpen menu item. Thesharpen command can increase the definition of edges (it is anunsharp mask), at the cost of increasing noise. 3.) For MacOS users, images now use Retina settings bydefault (go to Preferences to switch this off).Quote & Reply Reply Aug 24, 2017 08:08 AM Katharina KunzelmannScaling of overlaid valuesHi there,first of all thanks for that great tool! The 3D rendering is great!I have a question concerning the visualization of an overlay.I performed data analysis on fMRI data in SPM and used SnPM(non-parametrical toolbox for SPM) to do 2nd level analysis. Withthat, I also receive t-contrasts similar to those in SPM and I candisplay them as an overlay in MRIcroGL. I just have not found out,how they are scaled. The values don't make sense for any values Iwould imagine :) Mine are between .002 and 1. But what do theymean? My actual t-values would be around 3 and 4 and my actualp-values ConvertDicom to Nifti. This brings up the dicom2niix gui. After I selectmy output folder I get stuck. I cannot return to the main menu toselect my input files (dicoms). When the dicom2niix gui is open itprevents access to the MRIcroGL menu where I would be selecting mydicoms. Am I doing something wrong? ChristineQuote & Reply Reply Dec 20, 2018 09:12 PM Chris RordenRE: unable to covert dicoms using Windows version of MRIcroGLPlease make sure you are using the latest release (v1.2.20181114). You only need to select "output folder" once -that just tells the program where you want to save the covnerteddata. After that you drag and drop the DICOM folders onto thetoolbar of the dcm2niix GUI and it will convert the files for you.By the way, if you want to quickly view DICOM images (and do notcare about converting them), you can drag and drop the DICOM folderonto the main MRIcroGL window - unless the dcm2nii GUI dialog isvisible it assumes you just want to look at your images.Quote & Reply Reply Dec 20, 2018 09:12 PM Christine Smith RE: unable to covertdicoms using Windows version of MRIcroGL> Dear Chris,>Thank you for clearing that up. I didn't realized that the dcm2niixtoolbarwas waiting for me to drag and drop the files there.Best,ChristineQuote & Reply Reply Feb 27, 2019 10:02 PM Emily DennisOverlay misalignedI'm trying to make some figures but running into an odd andhopefully basic issue. I open my anatomical image then try to addthe statistics as an overlay but it appears to be centereddifferently. Viewing these files in other programs I don't havethis issue, so I know they are in the same space. Any thoughts onwhat might be causing this?Thanks,EmilyAttachment: overlay.png Quote & Reply Reply Feb 28, 2019 06:02 PM Emily DennisRE: Overlay misalignedIt appears this misalignment is an issue in the 2018 version. Inthe 2016 version I'm having a different issue - the overlay appearsto be aligned, but it won't show the range of values in the image.I'm trying to overlay a map of T-stats that I know range between -6and 6, but I'm getting 1 color. Help with either of these issues would be great - misalignment butproper values in 2018, proper alignment but not showing range ofvalues in 2016.ThanksAttachment: Tval.png Quote & Reply Reply Mar 1, 2019 02:03 PM Chris RordenRE: Overlay misaligned1. Can you provide the NIfTI image you are using as your overlay?2. Can you describe what "other programs" you are using?I think if you use SPM's Check Reg to look at this overlay, youwill see that it is not aligned to the background image. I thinkthe "other programs" you are using are ignoring the NIfTI S-form.Seeing the images will test this hypothesis.The one challenge with NIfTI is that it has two spatial transforms(the S-Form and the Q-Form). In situations where they both existand where they conflict different tools behavior differently. SPM,FSLEyes, MRIcroGL, etc give precedence to the S-Form (which makessense, as it has more degrees of freedom so is better for handlingregistrations). On the other hand, ITK based tools (Slicer, ANTS,etc) give precedence to the Q-Form. This means that images thatappear aligned with SPM may have a poor starting estimate for ANTS.For this reason, if you have multiple tools, it is worth settingthese to the same spatial transform (recognizing that the Q-Formcan not store shear transforms).Quote & Reply Reply Mar 4, 2019 10:03 PM Emily DennisRE: Overlay misalignedAh thank you that was it! I had been viewing it in FSL, I just hadto copy the qform/sform info to my stats image, now it works.Thank you!Quote & Reply Reply Apr 10, 2019 03:04 PM Elika BProblem with loading picture in MRIcroHi all,I want to change a DCOM picture to .nii one with MRIcroGL. I getthis error when I want to open .nii pic:This image file is smaller than described in header.Expected:131072 Selected:348.Could any one help please?Thanks!Quote & Reply Reply Apr 10, 2019 07:04 PM Chris RordenRE: Problem with loading picture in MRIcroCan you confirm you are using the latest version (v1.2.20181114)?If not, get it from here: You can view a DICOM image directly by dragging and dropping theDICOM image onto MRIcroGL. You can convert it to NIfTI by choosethe Import/ConvertDicomToNifti menu item and dragging the DICOMfile onto the conversion window. 131072 bytes sounds verysmall for a MRI scan - I assume this is only a single 2D slice. Youprobably want to convert a whole folder of 2D DICOMs to get 3Dvolumes.Quote & Reply Reply Jun 5, 2019 06:06 PM Maria Ironside - McLean HospitalTrying to launch in linux - GLXBadRenderRequestI'm trying to run mricrogl on my linux cluster and am getting thefollowing error when I try to launch it.> The program 'MRIcroGL' received an X Window System error.> This probably reflects a bug in the program.> The error was 'GLXBadRenderRequest'.> (Details: serial 676 error_code 160 request_code 148minor_code 1)> (Note to programmers: normally, X errors are reportedasynchronously;> that is, you will receive the error a while after causing it.> To debug your program, run it with the --sync command lineoption to> change this behavior. You can then get a meaningful backtracefrom> your debugger if you break on the gdk_x_error() function.)Quote & Reply Reply Jul 12, 2019 02:07 PM las nikolayCan MRIcroGL be compiled under the latest version of delphi?Can MRIcroGL be compiled under the latest version ofdelphi? What needs to be done?Quote & Reply Reply Jul 12, 2019 05:07 PM Chris RordenRE: Can MRIcroGL be compiled under the latest version of delphi?At one stage, MRIcroGL 1.0 could be compiled with either Delphi 7.0or Lazarus. I have not tested recent releases, but you coulddownload the final release source code and I suspect you could compile it with Delphiwithout much work.The modern MRIcroGL 1.2 uses OpenGL 3.3 Core instead of OpenGL 2.1,and I have never tried compiling this with Delphi. I would suggestensuring Delphi can support this version by compiling the basic OpenGL core project. If this works, I would think compiling the source code for MRIcroGL 1.2 would not take to much work - mainly translating the Lazarusformat form files (.lfm) to Delphi format (.dfm).I am really not sure there would be much benefit. The current codecompiles to Linux, Windows and MacOS using Lazarus and the timeconsuming tasks are completed using GLSL which would be identicalfor both compilers. So I expect this would be a lot of work forlittle gain.Quote & Reply Reply Jul 13, 2019 10:07 AM las nikolaycompile errorI downloaded the latest version of MRIcroGL12-1.2.20190410, whichwas compiled prompting the lack of some unit files, such asVectorMath, SimdUtils and so on. Can you check it? Thank youQuote & Reply Reply Jul 13, 2019 11:07 AM Chris RordenRE: compile errorPlease read the compiling section of the README.md file that comes with the repository(and is the project home page) - you will want to havethe Metal-Demos repository in your path and you will want toinstall the Python4Lazarus package in you IDE.Quote & Reply Reply Jul 15, 2019 05:07 AM las nikolayError in Save bitmap....1. With the compiled version 20190410 test, click File - > Savebitmap to report error. See attached file.2. With version 20190606, after compiling and testing, and clickingthe File drop-down menu, the error occur.See attached file.3. Can you add a progress bar for reading IMAGE files? Every timewhen open the software and load a larger file, the process takes alittle longer. It's better to have a progress bar.My test environment is: WIN7 x64ThanksAttachment: bug.rar Quote & Reply Reply Jul 18, 2019 03:07 PM Chris RordenRE: Error in Save bitmap....Thanks for the feedback.1.) [Windows specific issue with bitmap saves is fixed]( ) with latest commit. Please update both MRIcroGL12 and Metal-Demosrepositories.2.) Unable to replicate this issue. Can you test the latest commit.Also, does this issue influence the latest pre-compiled [stablerelease]( )? Can you provide feedback if this persists and open a Githubissue if you can provide any insight.3.) [I have created a feature request]( ) for progress feedback for Windows.I am afraid that my oldest computer has Windows 8.1. Be aware thatsupport for OpenGL was a bit shaky on older Intel integratedgraphics drivers for Windows. Modern graphics cards provide better3D Texture performance.Quote & Reply Reply Jul 18, 2019 03:07 PM Chris RordenRE: Trying to launch in linux - GLXBadRenderRequestWhat version are you attempting to run? I would first try version 1.2.20190410 which uses OpenGL 3.3. This modern version ensures all therequired extensions. If that does not work, try 1.0.20190410 which uses OpenGL 2.1. If that does not work, type "glxinfo" in the terminal tocheck details on your OpenGL support. You can fix most issues by reading through the trouble shooting page.Quote & Reply Reply Jul 19, 2019 05:07 AM las nikolayRE: Error in Save bitmap....1. I downloaded and tested the latest version. There are still somequestions about saving bitmap. See the video for details.Note: To reduce the size of the video, I saved the save bitmap to afixed location without a save dialog box.2. Can the Orientation Cube be marked S\I\A\P\L\R on each side?Attachment: bug2.rar Quote & Reply Reply Jul 19, 2019 12:07 PM Chris RordenRE: Error in Save bitmap....1.) Change the "Bitmap Zoom" in the preferences to 1 if you wantlower resolution bitmaps or your older computer is overwhelmed bythe huge bitmaps.2.) This would be a nice feature. The orientation cube code iscompletely modular, so you can update the simple cube project todevelop this. You could either do this with texture wrapping or bydrawing the text as triangles: -Demos/tree/master/cubeYou can issue a pull request when you are ready to share yoursolution with the rest of the community.Quote & Reply Reply Start New Topic 1 2 3 Next > v2.1.63-0
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